The reason licensed games usually fail at storytelling is that they try too hard to port the movie/game/book/whatever that they're based on straight across to the game, and this doesn't work. Gaming is a fundamentally interactive activity, while most media is fundamentally non-interactive, and this changes both the types of stories you can tell well and how best to do it.
To give only one example of how this works, let us examine the concept of game balance. A story like Naruto's has no concept of game balance, and in fact depends on imbalance: everyone's powers are ludicrously over the top, but some are clearly more over the top than others. This makes for good non-interactive storytelling, but it doesn't make for a good game. Game makers realize that a game needs to be balanced, and so they try to shoehorn balance into licensed stories. But this, in turn, should fundamentally alter the way the characters interact with one another, yet often it doesn't and so the story becomes less cohesive. End result: collapse.
This doesn't mean that games cannot be used for storytelling, of course. But games work best at telling a different kind of story than the "cinematic" non-interactive stories we see in movies and TV and books, and frankly they shouldn't try to be telling those types of stories: they just don't work well together. Games work best with a different kind of story, equally valid and just as good but perhaps less bombastic. But this is why licensed games are doomed to fail: to work well, a licensed game needs to tell a different kind of story than the one it is licensing, and that defeats much of the point of licensing in the first place.
Complexity is not depth. Machismo is not maturity. Obsession is not dedication. Tedium is not challenge. Support gaming: support the Wii.
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There is much to hate about modern gaming. That is why I support the Wii.
